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Sequence comparison with concave weighting functions.

作者信息

Miller W, Myers E W

出版信息

Bull Math Biol. 1988;50(2):97-120. doi: 10.1007/BF02459948.

DOI:10.1007/BF02459948

PMID:3207952

Abstract

摘要

相似文献

Sequence comparison with concave weighting functions.

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Methods Enzymol. 1988;164:765-93. doi: 10.1016/s0076-6879(88)64083-3.

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引用本文的文献

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Fast gap-affine pairwise alignment using the wavefront algorithm.

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Solving the master equation for Indels.

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Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map.

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Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform.

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Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps.

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Modular and configurable optimal sequence alignment software: Cola.

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本文引用的文献

Optimal sequence alignments.

Proc Natl Acad Sci U S A. 1983 Mar;80(5):1382-6. doi: 10.1073/pnas.80.5.1382.

Comparative biosequence metrics.

J Mol Evol. 1981;18(1):38-46. doi: 10.1007/BF01733210.

Identification of common molecular subsequences.

J Mol Biol. 1981 Mar 25;147(1):195-7. doi: 10.1016/0022-2836(81)90087-5.

An improved algorithm for matching biological sequences.

J Mol Biol. 1982 Dec 15;162(3):705-8. doi: 10.1016/0022-2836(82)90398-9.

Efficient sequence alignment algorithms.

J Theor Biol. 1984 Jun 7;108(3):333-7. doi: 10.1016/s0022-5193(84)80037-5.

Fast optimal alignment.

Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):175-9. doi: 10.1093/nar/12.1part1.175.

A general method applicable to the search for similarities in the amino acid sequence of two proteins.

J Mol Biol. 1970 Mar;48(3):443-53. doi: 10.1016/0022-2836(70)90057-4.

Alignment of three biological sequences with an efficient traceback procedure.

J Theor Biol. 1986 Aug 7;121(3):327-37. doi: 10.1016/s0022-5193(86)80112-6.

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相似文献

Sequence comparison with concave weighting functions.

Bull Math Biol. 1988;50(2):97-120. doi: 10.1007/BF02459948.

Computer analysis of nucleic acid sequences.

Methods Enzymol. 1988;164:765-93. doi: 10.1016/s0076-6879(88)64083-3.

Significance of protein sequence similarities.

Methods Enzymol. 1990;183:474-87. doi: 10.1016/0076-6879(90)83032-5.

Parametric sequence comparisons.

Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):6090-3. doi: 10.1073/pnas.89.13.6090.

Definition and identification of homology domains.

Comput Appl Biosci. 1988 Mar;4(1):25-33. doi: 10.1093/bioinformatics/4.1.25.

Parametric and inverse-parametric sequence alignment with XPARAL.

Methods Enzymol. 1996;266:481-94. doi: 10.1016/s0076-6879(96)66030-3.

Combined DNA and protein alignment.

Methods Enzymol. 1996;266:402-18. doi: 10.1016/s0076-6879(96)66025-x.

PRONUC: a software package for the analysis of protein and nucleic acid sequences.

Comput Methods Programs Biomed. 1987 Feb;24(1):27-36. doi: 10.1016/0169-2607(87)90062-9.

An algorithm for simultaneous comparison of several sequences.

Comput Appl Biosci. 1988 Mar;4(1):89-92. doi: 10.1093/bioinformatics/4.1.89.

Progressive alignment and phylogenetic tree construction of protein sequences.

Methods Enzymol. 1990;183:375-87. doi: 10.1016/0076-6879(90)83025-5.

引用本文的文献

Finding long tandem repeats in long noisy reads.

Bioinformatics. 2021 May 5;37(5):612-621. doi: 10.1093/bioinformatics/btaa865.

Fast gap-affine pairwise alignment using the wavefront algorithm.

Bioinformatics. 2021 May 1;37(4):456-463. doi: 10.1093/bioinformatics/btaa777.

Solving the master equation for Indels.

BMC Bioinformatics. 2017 May 12;18(1):255. doi: 10.1186/s12859-017-1665-1.

Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map.

BMC Bioinformatics. 2016 Mar 18;17:133. doi: 10.1186/s12859-016-0945-5.

Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform.

J Microbiol. 2015 Jan;53(1):60-9. doi: 10.1007/s12275-015-4601-y. Epub 2015 Jan 4.

Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps.

Int J Bioinform Res Appl. 2014;10(4-5):384-408. doi: 10.1504/IJBRA.2014.062991.

Modular and configurable optimal sequence alignment software: Cola.

Source Code Biol Med. 2014 Jun 9;9:12. doi: 10.1186/1751-0473-9-12. eCollection 2014.

Empirical assessment of sequencing errors for high throughput pyrosequencing data.

BMC Res Notes. 2013 Jan 22;6:25. doi: 10.1186/1756-0500-6-25.

Dissect: detection and characterization of novel structural alterations in transcribed sequences.

Bioinformatics. 2012 Jun 15;28(12):i179-87. doi: 10.1093/bioinformatics/bts214.

The construction and use of log-odds substitution scores for multiple sequence alignment.

PLoS Comput Biol. 2010 Jul 15;6(7):e1000852. doi: 10.1371/journal.pcbi.1000852.

本文引用的文献

Optimal sequence alignments.

Proc Natl Acad Sci U S A. 1983 Mar;80(5):1382-6. doi: 10.1073/pnas.80.5.1382.

Comparative biosequence metrics.

J Mol Evol. 1981;18(1):38-46. doi: 10.1007/BF01733210.

Identification of common molecular subsequences.

J Mol Biol. 1981 Mar 25;147(1):195-7. doi: 10.1016/0022-2836(81)90087-5.

An improved algorithm for matching biological sequences.

J Mol Biol. 1982 Dec 15;162(3):705-8. doi: 10.1016/0022-2836(82)90398-9.

Efficient sequence alignment algorithms.

J Theor Biol. 1984 Jun 7;108(3):333-7. doi: 10.1016/s0022-5193(84)80037-5.

Fast optimal alignment.

Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):175-9. doi: 10.1093/nar/12.1part1.175.

A general method applicable to the search for similarities in the amino acid sequence of two proteins.

J Mol Biol. 1970 Mar;48(3):443-53. doi: 10.1016/0022-2836(70)90057-4.

Alignment of three biological sequences with an efficient traceback procedure.

J Theor Biol. 1986 Aug 7;121(3):327-37. doi: 10.1016/s0022-5193(86)80112-6.